On 10/10/12 11:53 PM, Venkat Reddy wrote:
Dear all,
I am doing a protein-ligand simulation and following Justin's tutorials. I
have confusion in passing check point file to the next step in position
restrain simulation (during NPT). I am slowly releasing the restraints
during NPT simulation, *viz., 1000....100.....10....1....noPR*. So, during
NPT-PR, is it required to pass the check-point file generated in the
previous step to the next step (1000....100....10...1....noPR)? or is it
fine if I use directly the check point file generated during NPT-no PR step
to final MD step?
You seem to be asking two questions, so it's not really a matter of "or." One
should always pass the final checkpoint of the previous stage of simulation to
the current stage. So during your reduction of restraints, you should pass the
checkpoint from the previous restraint strength. At the outset of MD, you
should pass the checkpoint from whatever the step immediately prior to it was,
which, from the description, is NPT in the absence of restraints.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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